I dont have an ipod touch yet, but i know a jailbroken ipod uses cydia to get apps through wifi. But are there some apps that arent on cydia, and requre manual installation?

How would I go about doing that

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Yes, some apps are not in Cydia, so you will need to manually install them.
Download and install OpenSSH from Cydia.
Youll need to download the .deb file for the app.
Use an SSH program (WinSCP for windows, Cyberduck for mac)
Then connect to your ipod touch
Change connection type to sftp (server will be your ip address, username is root, password is alpine, root should be 22)
Then youll need to SSH the file into your device (i put it in my /tmp folder)
Then in WinSCP or Cyberduck, youll need to send this command "dpkg -i /tmp/file.deb"
Then it should install

Yes, some apps are not in Cydia, so you will need to manually install them.
Download and install OpenSSH from Cydia.
Youll need to download the .deb file for the app.
Use an SSH program (WinSCP for windows, Cyberduck for mac)
Then connect to your ipod touch
Change connection type to sftp (server will be your ip address, username is root, password is alpine, root should be 22)
Then youll need to SSH the file into your device (i put it in my /tmp folder)
Then in WinSCP or Cyberduck, youll need to send this command "dpkg -i /tmp/file.deb"
Then it should install